The plant rhizosphere plays a key role in plant function and immunity. Apple Replant Disease (ARD) is a dysbiosis in apple rhizosphere environments that have a history of apple cultivation. Due to increased intensification of apple growing systems and land scarcity, ARD incidence is on the rise and can result in a 50% loss of profitability to growers. Soil fumigation is a common practice for mitigating ARD, but has limited efficacy and is not allowed in some areas because of potential for environmental damage and human harm. Using resistant rootstocks is a key strategy in overcoming ARD. To understand rootstock resistance, it is important to describe and characterize the microbial communities of various rootstocks in an environment conducive to microbial health. We planted an organically managed apple orchard with 5 randomized repetitions of 15 different rootstocks. In both 2022 and 2023, we sampled the soil adhering to the roots of these trees for DNA extraction in order to characterize both bacterial and fungal microorganisms in the rhizosphere of the rootstocks in our research. We also established an aeroponic greenhouse trial (randomized with three repetitions) to sample rhizodeposits from 6 of the rootstocks used in the orchard trial, with the aim of characterizing metabolites with untargeted HPLC/LCMS. Bacterial phyla and genera differed in relative abundance between the rootstocks. A sparse PLS (partial least squares) discriminant analysis of rootstock exudates revealed differential sorting of some rootstocks. Neither study revealed clear biological indicators for ARD resistance, but the results evince that rootstock genotype does influence both microbial community and tree root exudation patterns.
